Lecture 25 (11/15/17)

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1 Lecture 25 (11/15/17) Reading: Ch9; Ch25; , Problems: Ch9 (study-guide: applying); 1,2 Ch9 (study-guide: facts); 7,8 Ch25 (text); 1-3,5-7,9,10,13-15 Ch25 (study-guide: applying); 1,4 Ch25 (study-guide: facts); 3,4,6 NEXT Reading: Ch26; Problems: Ch26 (text); 1,2,5,6,12 Ch26 (study-guide: applying); 1 Ch8 (study-guide: facts); 1,3,5 Nucleic Acids A. Recombinant DNA: Biochemical Basis of Biotechnology 1. Restriction enzymes, DNA ligase 2. Vectors and Inserts to make recombinant DNA (rdna) a. Inserts i. cdna ii. Genomic b. Vectors 3. Transformation of hosts 4. Selection of transformants a. Selectable marker/gene b. Distinguish empty plasmids i. Loss of resistance ii. Reporter gene 5. Expression a. Special vectors b. Fusion proteins i. purification ii. labeling 6. Site-directed mutagenesis B. Replication 1. Polymerases 2. Fidelity 3. Sequence determination Recombinant DNA is DNA made in the laboratory that is derived from at least two genetic sources. Biochemical Basis of Biotechnology - Restriction enzymes, DNA ligase - Vectors and Inserts to make recombinant DNA (rdna) - Transformation of hosts - Selection of transformants - Expression - Site-directed mutagenesis 1

2 Restriction enzymes are used to cut DNA into fragments, which then are spliced together in new combinations. DNA ligase catalyzes the joining of DNA fragments. Restriction Sites Restriction enzymes recognize palindromic DNA sequences: 5ʼ.G-3ʼ 5ʼ.GAATTC 3ʼ 3ʼ.CTTAA-5ʼ 3ʼ.CTTAAG 5ʼ 5ʼ-AATTC 3ʼ 3ʼ-G 5ʼ Some make straight cuts, others make staggered cuts, resulting in overhangs or sticky ends. EXAMPLES: 2

3 Restriction Sites Restriction enzymes recognize palindromic DNA sequences: 5ʼ.GAATTC 3ʼ 3ʼ.CTTAAG 5ʼ Some make straight cuts, others make staggered cuts, resulting in overhangs or sticky ends. EXAMPLES: Restriction Endonucleases EcoRI Endonuclease EcoRI endonuclease PDBid 1ERI EcoRV Endonuclease EcoRV endonuclease PDBid 4RVE 3

4 Restriction Endonucleases Cleave at Specific Recognition Sites Restriction Endonucleases Key to Making rdna Molecules DNA Ligase will seal the nick by making the covalent phosphodiester bond 4

5 DNA Ligase: Also Key to Making rdna Molecules DNA Ligase Reaction 5

6 Restriction Endonucleases & DNA Ligase: Key to Making rdna Molecules Process Diagram: Recombinant DNA Construction Recombinant DNA molecule Where does this Foreign DNA come from and how is it purified? Vectors and Inserts DNA fragments used for molecular cloning come from two sources: Genomic DNA cdna (Copy DNA or complementary DNA)From reverse transcription of mrna A genomic clone contains the gene(s) as a fragment of the genome of an organism. The DNA is cut into fragments by restriction enzymes, and each fragment is inserted into a vector. Represents an mrna from a given cell/tissue. cdna is produced by making a DNA copy of the mrna population using the RNAdirected DNA polymerase called, reverse transcriptase. A cdna library is a snapshot of the transcription pattern of the cell. cdna clones are used to provide the ORF for expressing the protein A genomic clone A cdna clone 6

7 Vectors and Inserts: cdna Cloning Vectors and Inserts: cdna Cloning 7

8 How do you find your DNA of interest? Restriction Digest Electrophoretogram Process Diagram: Southern Blotting Using polynucleotide kinase and g- 32 P-ATP Biochemical Basis of Biotechnology - Restriction enzymes, DNA ligase - Vectors and Inserts to make recombinant DNA (rdna) - Transformation of hosts - Selection of transformants - Expression - Site-directed mutagenesis All vectors have 3 things: 1. Autonomous replication ability 2. Selection for hosts that contain vector 3. Site for insertion of rdna Viruses as vectors (bacteriophage or retroviruses). Viruses can be altered to attenuate some detrimental genes in the virus (e.g., those that kill the host). Viruses can be altered to carry recombinant DNA into cells 8

9 Biochemical Basis of Biotechnology - Restriction enzymes, DNA ligase - Vectors and Inserts to make recombinant DNA (rdna) - Transformation of hosts - Selection of transformants Transformation: - Expression by inserting it into Recombinant host cells (transfection DNA is cloned if host -cells Site-directed are from an animal). mutagenesis Second key discovery in biotechnology. Usually only a few cells are transformed (1 cell in 10,000). Reason for the need for a selectable marker. The first host cells used were bacteria, especially E. coli. Yeasts (Saccharomyces) are commonly used as eukaryotic hosts. Inserting the recombinant DNA into a cell: Cells may be treated with chemicals to make plasma membranes more permeable DNA diffuses into cells. Electroporation a short electric shock creates temporary pores in membranes, and DNA shoots to the + end and can enter cells. Biochemical Basis of Biotechnology - Restriction enzymes, DNA ligase - Vectors and Inserts to make recombinant DNA (rdna) - Transformation of hosts - Selection of transformants - Expression - Site-directed mutagenesis Use of antibiotic resistance gene (e.g., ampicilin resistance) on a plasmid For viral vectors, use of infected phenotype. Use of selectable markers to detect either insertion into the vector or incorporation into the host. Some of these are a type of reporter gene a gene whose expression is easily observed. Many plasmids contain the lacz gene with a multiple cloning site within its sequence. lacz codes for an enzyme that can convert the substrate X-Gal into a bright blue product Plasmid Cloning Video How can you distinguish between recdna vectors and empty vectors? 9

10 DNA Cloning Introduce DNA into Organism Use of pbr322 to clone foreign DNA in E. coli and identify cells containing it. Antibiotic Selection Antibiotics, such as penicillin and ampicillin, kill bacteria. Plasmids can carry genes that give a host bacterium a resistance against antibiotics. Allows growth (selection) of bacteria that have taken up the plasmid O OH N O O S H N H H N H Ampicillin Identification of Empty Plasmids P lac Insert ORF of interest Origin of replication Antibiotic resistance gene Multiple cloning site Promoter for transcription, translation (host specific) Ori Recombinant DNA Clone Insert Makes b-galactosidase +Insert Doesn t make b-galactosidase N/A N/A 10

11 Biochemical Basis of Biotechnology - Restriction enzymes, DNA ligase - Vectors and Inserts to make recombinant DNA (rdna) - Transformation of hosts - Selection of transformants - Expression - Site-directed mutagenesis Expression vectors include sequences needed for expression of a transgene in a host cell. For prokaryote host, which are preferred for making large amounts: A bacterial promoter, ribosome binding site, and a transcription termination signal, must all be included. For eukaryote (mostly yeast): The eukaryotic promoter/enhancer and terminator (poly-a addition signal/site) must be included. These can also be: Inducible promoters which respond to a specific signal Tissue-specific promoters expressed only in certain tissues at certain times Signal sequences e.g., a signal to secrete the product to the extracellular medium Typical Expression Vector Can you use such an expression system to help in purification? 11

12 Purification of Recombinant Proteins Purification of natural proteins is difficult. Recombinant proteins can be tagged for purification. The tag binds to the affinity resin, binding the protein of interest to a purification column. TABLE 9-3 Commonly Used Protein Tags Tag protein/peptide Molecular mass (kda) Immobilized ligand Protein A 59 Fc portion of IgG (His) Ni 2+ Glutathione-S-transferase (GST) 26 Glutathione Maltose-binding protein 41 Maltose β-galactosidase 116 Chitin-binding domain 5.7 Chitin p-aminophenyl-β-dthiogalactoside (TPEG) Affinity Chromatography Basis = Biotechnology (recombinant DNA technology) has function revolutionized protein purification. At the level of the DNA sequence, the DNA sequence encoding such binding proteins or tags can be fused to the sequence encoding YFP. In this way, a chimeric protein is produced that has the binding function, which allows the use of affinity chromatography. Common tags are: Column beads have attached: Maltose-binding protein Maltose Chitin-binding protein Chitin Glutathione-S-transferase Glutathione (g-glu-cys-gly) His-His-His-His-His-His Ni-chelate 12

13 Purification of Recombinant Proteins Can you use such an expression system to help visualize proteins INSIDE of cells? Expression EXAMPLE: Green fluorescent protein, which normally occurs in a jellyfish, emits visible light when exposed to UV light. The gene for this protein has been isolated and incorporated into vectors as a reporter gene arac operator P BAD 13

14 GFP Tagged Protein Localization YES! Fluorescence Can Be Used to Determine Protein Location In Vivo Green fluorescent protein (GFP) use recombinant DNA technologies to attach GFP to protein of interest visualize with a fluorescent microscope Immunofluorescence tag protein with primary antibody and detect with secondary antibody containing fluorescent tag Protein can also be fused to a short epitope (e.g., myc-tag [EQKLISEEDL], HA-tag [YPYDVPDYA] or Flag-tag [DYKDDDDK]), and the primary antibody detecting the epitope can be fluorescently labeled. 14